Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different ’catchments’ and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health

Report On Higher Education

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A comparative judgement approach to teacher assessment

This is an Accepted Manuscript of an article published by Taylor & Francis in Assessment in Education: Principles, Policy and Practice on 16th October 2014 available online: http://dx.doi.org/10.1080/0969594X.2014.978839We report one teacher’s response to a top-down shift from external examinations to internal teacher assessment for summative purposes in the Republic of Ireland. The teacher adopted a comparative judgement approach to the assessment of secondary students’ understanding of a chemistry experiment. The aims of the research were to investigate whether comparative judgement can produce assessment outcomes that are valid and reliable without producing undue workload for the teachers involved. Comparative judgement outcomes correlated as expected both with test marks and with existing student achievement data, supporting the validity of the approach. Further analysis suggested that teacher judgement privileged scientific understanding, whereas marking privileged factual recall. The estimated reliability of the outcome was acceptably high, but comparative judgement was notably more time-consuming than marking. We consider how validity and efficiency might be improved and the contributions that comparative judgement might offer to summative assessment, moderation of teacher assessment and peer assessment